Contacts of the strand formed by residues 375 - 384 (chain A) in PDB entry 4TLG
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 375 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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283A SER* 3.4 5.3 - - - -
284A VAL* 2.7 39.9 + - + +
309A SER* 5.0 4.7 - - - -
310A ASP 3.5 4.5 - - - +
311A GLY 3.6 29.2 - - - -
312A GLY* 3.8 7.4 - - - +
313A ASP* 2.8 40.5 + - - +
314A ILE* 4.2 13.0 - - + -
367A ASN* 2.8 37.7 + - - +
369A TYR* 4.1 1.4 + - - -
370A SER* 3.8 11.5 + - - -
373A HIS* 3.8 16.8 - - - -
374A ALA* 1.3 78.9 - - - +
376A LYS* 1.3 63.8 + - - +
377A LEU* 5.8 0.9 - - + -
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Residues in contact with LYS 376 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281A THR* 3.7 27.8 - - + -
282A ARG 3.7 7.0 - - - +
283A SER* 4.5 8.5 - - - +
309A SER* 3.2 6.8 - - - -
310A ASP* 2.8 52.6 + - + +
375A LYS* 1.3 74.0 - - - +
377A LEU* 1.3 61.7 + - - +
378A SER* 4.3 1.6 - - - +
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Residues in contact with LEU 377 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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280A HIS 3.9 0.2 - - - +
281A THR* 3.2 4.0 - - - -
282A ARG 2.8 44.5 + - - +
284A VAL* 4.3 11.9 - - + -
290A LEU* 3.8 13.0 - - + -
307A PHE* 4.2 14.8 - - + -
308A ALA 3.4 16.4 - - - +
309A SER* 4.7 2.7 - - - -
314A ILE* 4.4 13.7 - - + -
365A PHE* 3.4 55.0 - - + -
375A LYS* 4.0 1.8 - - + -
376A LYS* 1.3 74.9 - - - +
378A SER* 1.3 61.6 + - - +
379A TYR* 3.8 22.8 - - + -
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Residues in contact with SER 378 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
278A TYR* 3.7 29.1 - - - -
280A HIS 3.1 9.0 - - - -
281A THR* 2.9 23.3 + - - +
307A PHE* 3.2 5.0 - - - +
308A ALA* 2.9 37.2 + - - +
376A LYS* 4.3 1.4 - - - +
377A LEU* 1.3 73.9 - - - +
379A TYR* 1.3 63.4 + - - +
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Residues in contact with TYR 379 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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278A TYR* 3.7 6.5 - - - +
279A GLU* 3.2 4.9 + - - +
280A HIS* 2.8 67.8 + + + +
282A ARG* 3.5 43.1 + - + -
290A LEU* 4.0 17.2 - - + +
292A VAL* 3.8 29.8 - - + +
306A GLN 3.3 11.7 - - - +
307A PHE* 3.9 9.2 - - + -
365A PHE* 4.3 10.8 - + + -
377A LEU* 3.8 20.4 - - + -
378A SER* 1.3 75.5 - - - +
380A THR* 1.3 66.2 + - - +
381A VAL* 4.0 17.9 - - + -
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Residues in contact with THR 380 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LYS* 4.9 9.1 - - + +
277A GLN 3.9 4.3 + - - -
278A TYR* 3.4 8.2 - - - -
279A GLU* 2.9 38.1 + - + +
304A ARG 5.6 0.4 - - - +
305A TRP* 3.2 5.4 - - - -
306A GLN* 3.0 47.4 + - + +
379A TYR* 1.3 71.8 - - - +
381A VAL* 1.3 67.1 + - - +
382A GLU* 3.8 31.0 - - + +
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Residues in contact with VAL 381 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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279A GLU* 4.5 9.6 + - - +
280A HIS* 5.8 0.8 - - - -
292A VAL* 4.2 20.4 - - + -
294A ASN* 3.7 24.8 + - - +
303A LEU* 4.4 12.6 - - + -
304A ARG 3.6 6.3 - - - +
305A TRP* 4.2 3.4 - - + -
306A GLN 5.7 0.2 - - - +
363A LEU* 3.6 36.1 - - + -
365A PHE* 5.0 4.0 - - + -
379A TYR* 4.0 22.8 - - + -
380A THR* 1.3 80.6 - - - +
382A GLU* 1.3 65.9 + - - +
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Residues in contact with GLU 382 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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165A LYS* 3.0 22.7 + - - +
279A GLU* 5.5 2.0 - - - +
302A VAL 3.7 0.9 - - - +
303A LEU* 3.5 7.5 - - - +
304A ARG* 2.9 69.3 + - + +
380A THR* 3.8 20.0 - - + +
381A VAL* 1.3 78.8 - - - +
383A VAL* 1.3 64.0 + - - +
384A LEU* 3.9 16.6 + - + +
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Residues in contact with VAL 383 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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294A ASN* 3.7 39.9 - - + +
295A GLU 5.4 2.9 - - - +
296A ILE* 3.6 24.0 - - + -
301A CYS* 4.3 7.6 - - + -
302A VAL 3.5 4.7 - - - +
303A LEU* 3.9 10.3 - - + -
382A GLU* 1.3 73.5 - - - +
384A LEU* 1.3 64.4 + - - +
385A LEU* 3.8 28.6 + - + +
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Residues in contact with LEU 384 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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163A LEU* 4.2 17.3 - - + -
200A VAL* 3.9 18.2 - - + +
204A LEU* 4.0 27.8 - - + -
301A CYS* 3.5 6.4 - - - -
302A VAL* 2.7 52.3 + - + +
304A ARG* 4.1 42.0 - - + +
382A GLU* 3.9 24.0 - - + +
383A VAL* 1.3 76.6 - - - +
385A LEU* 1.3 62.8 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il